Finding complementarity between mRNA and rRNA using BLAST

Question

[Ali]

Hi

I am new to bioinformatics. I am trying to find complementarity between mRNAs and rRNAs.

Precisely, I have a list of 5'UTR mRNAs and I want to find the mRNAs that have complementarity as long as at least 5 nucleotide with a specific rRNA (say 18S).

Since as far as I understood, web BLAST just gives the similar sequences and not the complementary sequences, I got the reverse-complementary sequence of 18S rRNA and pasted that to the query section of BLAST. I also had a .fasta file containing the 5'UTR mRNAs which I could upload to the BLAST web page. But every time I do this (in blastn) I receive a "Bad gateway" error (Error 502) .

I have two questions here:

1. Why am I receiving this error?

2. How can I specify that I just want 5 similar nucleotide (between mRNAs and rRNA) in the sequence? Is it possible at all using BLAST?

Thank you very much!

[Devon Ryan]

Out of curiousity, what's the biological background for this? Complementarity between rRNA and an mRNA isn't known to have any biological relevance (to my knowledge) and if one allows as few as 5 nucleotide long matches then one would expect every mRNA to have at least one matching site.

BTW, blast checks the reverse complement of whatever you input as well.

[piet]

In prokaryotes, the 3'-terminal residues of the 16S-rRNA are the so called Shine-Dalgarno sequence. This sequence stretch helps the ribosome to locate the start codon in the mRNA. Most bacterial start codons are preceded by an AG rich pattern vaguely similar to the 3' end of rrs. However, nucleotide blast is not suited to detect this kind of similarity.

[Devon Ryan]

Figures that prokaryotes would have something like that :P

[Ali]

Regulation of gene expression. Well, 5 is just an example. I just want to know how can I find those mRNAs that have a specific number of similar/complement consecutive nucleotide with the sequence of my interest. There exist mRNAs that might have no similarities.

and could you please tell me how can I check the reverse complement of a sequence? Is this option available in the web version or in the BLAST+?

Answer 1

[piet]

could you please tell me how can I check the reverse complement of a sequence? Is this option available in the web version or in the BLAST+?

Please read the Blast+ documentation carefully. You should also read about the word size in blast which is 11 by default. You should use blast only for query sequences which are substancially longer than the word size.

Blast searches your query in both strands of its database by default, but you may use options to restrict search to one strand.

[Ali]

Thanks! I think I'm figuring out how it works. Yes apparently the smallest word size for comparing 2 nucleotide sequence is 7 so I should go with that.